Semantic search over the corpus. Returns chunks with page-level citations.

Args: query: natural-language question or topic. top_k: number of results (default 6). doc_id: restrict to one document (from list_documents), "" = all. note_type: which payload types to search — "raw" (verbatim paper text, ground truth), "claude_note" (Claude's reading notes), "hyde" (generated HyDE bridges only), "all" (raw + claude_note, the default), or "everything" (raw + claude_note + hyde). hypothesis: HyDE fallback. When the plain query misses (low scores), pass a short hypothetical answer paragraph here. It is embedded and averaged with the query (Gao et al., 2023) to retrieve REAL corpus chunks via the hypothesis. Each hit is tagged retrieved_via="hyde". "" = ordinary query-vector search (retrieved_via="direct").

Persist a HyDE hypothetical document as a reusable type=hyde bridge.

Use after a search(query, hypothesis=...) fallback produced good grounding, so the same retrieval miss becomes an indexed hit next time (searchable via note_type="hyde" or "everything"). A hyde bridge is generated text, never a citable source. Idempotent per (doc_id, query) — re-saving updates in place.

Args: query: the user query this hypothesis answers (used for the bridge id). hypothesis: the hypothetical answer paragraph to store and embed. doc_id: optional document this bridge is about ("" = corpus-wide). title: optional label ("" = derived from the query).

List all documents in the knowledge base with doc_id, title, and pages.

Full text of one page of a document — for reading context around a search hit.

Args: doc_id: document id from search/list_documents. page: 1-based page number.

APA-7 citation for a document: in-text (parenthetical + narrative) and the full reference-list entry. Use these verbatim when writing — the corpus is APA only, never mix styles. For a direct quote, add the page to the in-text form: '(Author, Year, p. N)'.

Args: doc_id: document id from search/list_documents.

Render a PDF page as an image, optionally with a passage highlighted. Use after search/get_page to SHOW the user the exact source location.

Args: doc_id: document id from search/list_documents. page: 1-based page number. highlight: passage to highlight. Verbatim raw-chunk text from search() always works; paraphrases usually work too — matching falls back exact -> sentence pieces -> fuzzy word alignment -> semantic (embeds the text and highlights the nearest raw chunk on this page). Returns the image plus a highlight_method report. "" = no highlighting.